title: ChIP-Seq analysis of H3K27me3 in human Mobilized CD34 cells; DNA_Lib 258

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 258
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8641
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772951_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 258-DNA_Lib 258-DNA_Lib 258-DNA_Lib 258-DNA_Lib 258.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10658
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,089,185
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2126
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2862
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9724
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4361
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.87

**********************************************************************

ANALYSIS FILE NAME: GSM772951_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 258-DNA_Lib 258-DNA_Lib 258-DNA_Lib 258-DNA_Lib 258.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10922
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MCD34 H3K27me3 36 58
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01536 Library DNA_Lib 258 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,089,185
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2126
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.2862
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9724
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4361
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.87

**********************************************************************

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 258

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in human HUES64 cells; Lib EpiLabSPL Row 1709

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1709
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8068
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772807_BI.HUES64.Input.Lib_EpiLabSPL_Row_1709.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1709.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1709, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10850
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,863,755
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.005
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0345
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0796
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

ANALYSIS FILE NAME: GSM772807_BI.HUES64.Input.Lib_EpiLabSPL_Row_1709.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1709.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1709, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11114
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES64 Input 09
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line ChIP-Seq Input Library Lib EpiLabSPL Row 1709 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,863,755
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.005
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.0345
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0796
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

molecule: genomic DNA

organism: Homo sapiens

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1709

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: HUES64 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: molecule

value: genomic DNA

tag: disease

tag: passage

tag: line

tag: batch

value: ES cell HUES_64-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of WCE in human HUES48 cells; Lib EpiLabSPL Row 1710

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1710
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8055
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772794_BI.HUES48.Input.Lib_EpiLabSPL_Row_1710.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1710.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1710, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10842
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,681,221
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0207
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0548
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

ANALYSIS FILE NAME: GSM772794_BI.HUES48.Input.Lib_EpiLabSPL_Row_1710.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1710.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1710, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11106
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES48 Input 10
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line ChIP-Seq Input Library Lib EpiLabSPL Row 1710 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,681,221
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0207
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0548
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1710

value: HUES48 stem cells

value: HUES48 Cell Line

value: ES cell HUES_48-1


title: ChIP-Seq analysis of WCE in human HUES64 cells; Lib EpiLabSPL Row 1726

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1726
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8015
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772754_BI.HUES64.Input.Lib_EpiLabSPL_Row_1726.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1726.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1726, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10609
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,319,620
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0057
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0373
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

ANALYSIS FILE NAME: GSM772754_BI.HUES64.Input.Lib_EpiLabSPL_Row_1726.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1726.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1726, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10873
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES64 Input 26
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line ChIP-Seq Input Library Lib EpiLabSPL Row 1726 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,319,620
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0038
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0057
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0373
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1726

value: HUES64 Cell Line

value: ES cell HUES_64-2


title: ChIP-Seq analysis of H3K4me3 in human HUES48 cells; Lib EpiLabSPL Row 1714

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1714
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8058
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8177
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772797_BI.HUES48.H3K4me3.Lib_EpiLabSPL_Row_1714.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1714.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1714, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10798
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,474,846
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.304
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.338
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9991
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3971
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

ANALYSIS FILE NAME: GSM772797_BI.HUES48.H3K4me3.Lib_EpiLabSPL_Row_1714.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1714.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1714, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11062
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES48 H3K4me3 14
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K4me3 Library Lib EpiLabSPL Row 1714 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,474,846
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.304
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.338
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9991
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3971
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.93

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1714

value: embrionic stem cell

value: KSR

value: ES cell HUES_48-2

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27me3 in human HUES64 cells; Lib EpiLabSPL Row 1722

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1722
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8011
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772750_BI.HUES64.H3K27me3.Lib_EpiLabSPL_Row_1722.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1722.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1722, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10688
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,657,489
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2689
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2897
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9987
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

ANALYSIS FILE NAME: GSM772750_BI.HUES64.H3K27me3.Lib_EpiLabSPL_Row_1722.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1722.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1722, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10952
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES64 H3K27me3 22
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K27me3 Library Lib EpiLabSPL Row 1722 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,657,489
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2689
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2897
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9987
IROC_PERCENTILE: 94
POISSON_SCORE: 0.3546
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.96

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1722

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: SDS lysis

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE

status: Public on Dec 05 2011

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7514
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM773048_BI.Mobilized_CD34_Primary_Cells.Input.RO_01517.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01517 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8252
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,174,619
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0032
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0077
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0318
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

ANALYSIS FILE NAME: GSM773048_BI.Mobilized_CD34_Primary_Cells.Input.RO_01517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01517 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8279
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 Input 17
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01517 Library Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized Mobilized CD34:WCE EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,174,619
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0032
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0077
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0318
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.92

**********************************************************************

source_name: flow sorted CD34+ cells, mobilized; Lib:RI:20100524:01--ChIP:MA:20100517:01:Mobilized CD34:WCE

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 43

value: Male

value: Caucasian

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human HUES64 cells; Lib EpiLabSPL Row 1720

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1720
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8013
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772752_BI.HUES64.H3K4me3.Lib_EpiLabSPL_Row_1720.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1720.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES64 Cell Line, Library Lib EpiLabSPL Row 1720, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10693
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,314,943
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6561
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6537
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9989
IROC_PERCENTILE: 48
POISSON_SCORE: 0.6661
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM772752_BI.HUES64.H3K4me3.Lib_EpiLabSPL_Row_1720.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1720.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib EpiLabSPL Row 1720, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10957
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES64 H3K4me3 20
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K4me3 Library Lib EpiLabSPL Row 1720 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,314,943
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6561
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6537
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9989
IROC_PERCENTILE: 48
POISSON_SCORE: 0.6661
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1720

value: HUES64 Cell Line

value: embrionic stem cell

value: KSR

value: genomic DNA

value: ES cell HUES_64-2

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in human HUES48 cells; Lib EpiLabSPL Row 1725

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1725
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8016
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8177
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772755_BI.HUES48.Input.Lib_EpiLabSPL_Row_1725.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1725.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1725, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10600
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,183,395
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0215
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

ANALYSIS FILE NAME: GSM772755_BI.HUES48.Input.Lib_EpiLabSPL_Row_1725.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1725.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1725, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10864
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES48 Input 25
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line ChIP-Seq Input Library Lib EpiLabSPL Row 1725 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,183,395
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0215
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.95

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1725

value: HUES48 stem cells

value: HUES48 Cell Line

value: ES cell HUES_48-2

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: SDS lysis


title: ChIP-Seq analysis of H3K27me3 in human HUES48 cells; Lib EpiLabSPL Row 1716

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1716
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8027
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8177
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM772766_BI.HUES48.H3K27me3.Lib_EpiLabSPL_Row_1716.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1716.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1716, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10650
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,646,703
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2249
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.276
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9946
IROC_PERCENTILE: 88
POISSON_SCORE: 0.3517
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM772766_BI.HUES48.H3K27me3.Lib_EpiLabSPL_Row_1716.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1716.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1716, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10914
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: HUES48 H3K27me3 16
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K27me3 Library Lib EpiLabSPL Row 1716 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,646,703
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2249
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.276
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9946
IROC_PERCENTILE: 88
POISSON_SCORE: 0.3517
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1716

value: embrionic stem cell

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in Mobilized CD34 cells; Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized CD34:H3K27Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized CD34:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7512
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM773046_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01517.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized CD34:H3K27Me3.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01517 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8229
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,178,605
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1534
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3212
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9364
IROC_PERCENTILE: 36
POISSON_SCORE: 0.3926
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.84

**********************************************************************

ANALYSIS FILE NAME: GSM773046_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized CD34:H3K27Me3.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01517 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8256
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 H3K27me3 17
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01517 Library Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized Mobilized CD34:H3K27Me3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,178,605
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1534
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.3212
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9364
IROC_PERCENTILE: 36
POISSON_SCORE: 0.3926
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.84

**********************************************************************

source_name: flow sorted CD34+ cells, mobilized; Lib:RI:20100524:06--ChIP:MA:20100517:06:Mobilized CD34:H3K27Me3

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 43

value: Male

value: Caucasian


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized CD34:WCE

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7511
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM773045_BI.Mobilized_CD34_Primary_Cells.Input.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized CD34:WCE.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01562 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8251
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,833,618
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0051
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0329
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.91

**********************************************************************

ANALYSIS FILE NAME: GSM773045_BI.Mobilized_CD34_Primary_Cells.Input.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized CD34:WCE.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01562 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8278
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 Input 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01562 Library Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized Mobilized CD34:WCE EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,833,618
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0051
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0329
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.91

**********************************************************************

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:06--ChIP:MA:20100517:06:Mobilized CD34:WCE

value: 42 years

value: standard

value: ChIP-Seq Input

value: Input


title: Bernstein_HSMM_Control (superseded by GSE136426)

status: Public on Jun 02 2011

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
****************************
GSM733663 record metadata submitted on May 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE136426
****************************

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

source_name: HSMM

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

value: skeletal muscle myoblasts

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: antibody

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: replicate


title: ChIP-Seq analysis of H3K27me3 in HUES64 cells; Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3

status: Public on Mar 31 2011

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5715
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669974_BI.HUES64.H3K27me3.Lib_MC_20101025_04--ChIP_MC_20101020_04_ES_cell_HUES_64_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6499
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4448
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4804
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9883
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 100

**********************************************************************

ANALYSIS FILE NAME: GSM669974_BI.HUES64.H3K27me3.Lib_MC_20101025_04--ChIP_MC_20101020_04_ES_cell_HUES_64_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6709
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES64 H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K27me3 Library Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.4448
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4804
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9883
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 100

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:04--ChIP:MC:20101020:04:ES cell HUES_64:H3K27Me3

tag: sample alias

tag: sample common name

value: HUES64 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: molecule

value: genomic DNA

tag: disease

tag: passage

tag: line

tag: batch

value: ES cell HUES_64-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: NME-Pre TGF-3

status: Public on Jan 30 2014

type: RNA

city: West Lafayette

first: Michael

last: Wendt

state: IN

address: 201 S. University St.

department: MCMP

institute: Purdue University

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16hr at 45C on GeneChip Murine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanned dat files were converted to cel files using Affymetrix propriatary software Expression Console (EC). EC was also used to convert the cel files into spreadsheets of gene expression numbers using the RMA (Robust Multigene Analysis) feature of EC (RMA normalized data provided in sample table).  Raw data in logbase2 were converted into linear values and exported as a tab delimited text file along with appropriate annotations. Gene expression changes were defined as follows: The  group means were calculated for each gene.  Binary comparisons were generated  in which the group-mean ratio s were calculated for each gene. Raw data, group-means and group-mean ratios were imported into MS access data base manager. record were filtered for ratios >= 1.5 or <= 0.666666. Raw data (linear ) for each group were imported into BAMarray (Bayesian Analysis of Microarray data), a bootstrapping software  that uses z-values to confer statistical significance upon observed differences in the measurements.  Results for BAM analysis were imported into the same Access database and the BAM results cross-referenced to the group-mean ratios. Records that met both the group-mean ratio magnitude and BAM significance were deemed to be the differentially expressed genes (provided in the 'differentially_expressed.txt' series supplementary file)

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: NME-Pre TGF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical manual, 2001, Affymetrix)

growth_protocol: DMEM containing 10% FBS and 10mg/ml Insulin

extract_protocol: Quaigen RNAeasy

treatment_protocol: 5 ng/ml TGF-beta1 for 4 weeks added every 4 days, then exogenous TGF-beta1 was withdrawn and cells were cultured for an additional 4 weeks.

tag: cell line background

value: NMumG

tag: cell type

value: normal murine mammary gland cells

tag: transformed by

value: overexpression of EGFR (NME)

tag: stimulated with

value: none (unstimuated control)


title: ChIP-Seq analysis of H3K4me3 in Mobilized CD34 cells; Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized CD34:H3K4Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7507
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM773041_BI.Mobilized_CD34_Primary_Cells.H3K4me3.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized CD34:H3K4Me3.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01562 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8241
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,610,929
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.7325
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7285
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.998
IROC_PERCENTILE: 25
POISSON_SCORE: 0.745
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM773041_BI.Mobilized_CD34_Primary_Cells.H3K4me3.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized CD34:H3K4Me3.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01562 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8268
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 H3K4me3 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01562 Library Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized Mobilized CD34:H3K4Me3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,610,929
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
FINDPEAKS_SCORE: 0.7325
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7285
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.998
IROC_PERCENTILE: 25
POISSON_SCORE: 0.745
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:08--ChIP:MA:20100517:08:Mobilized CD34:H3K4Me3

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 42 years

value: Male

value: Caucasian

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27me3 in HUES 6 cells; Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5626
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669897_BI.HUES6.H3K27me3.Lib_XZ_20101004_11--ChIP_XZ_20100930_11_ES_cell_HUES_6_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6544
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3693
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.3981
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9772
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5
POISSON_PERCENTILE: 90

**********************************************************************

ANALYSIS FILE NAME: GSM669897_BI.HUES6.H3K27me3.Lib_XZ_20101004_11--ChIP_XZ_20100930_11_ES_cell_HUES_6_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6754
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 H3K27me3 e3.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K27me3 Library Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3693
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.3981
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9772
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5
POISSON_PERCENTILE: 90

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:11--ChIP:XZ:20100930:11:ES cell HUES_6:H3K27Me3

value: HUES6 Cell Line

value: embrionic stem cell

value: KSR

value: HUES 6

value: ES cell HUES_6-2

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis


title: ChIP-Seq analysis of WCE in HUES 6 cells; Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5624
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669895_BI.HUES6.Input.Lib_XZ_20101004_14--ChIP_XZ_20100930_14_ES_cell_HUES_6_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the HUES6 Cell Line, Library Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6539
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0299
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0756
POISSON_PERCENTILE: 77

**********************************************************************

ANALYSIS FILE NAME: GSM669895_BI.HUES6.Input.Lib_XZ_20101004_14--ChIP_XZ_20100930_14_ES_cell_HUES_6_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6749
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 Input CE.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line ChIP-Seq Input Library Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.0299
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0756
POISSON_PERCENTILE: 77

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:14--ChIP:XZ:20100930:14:ES cell HUES_6:WCE

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: Bernstein_HMEC_Control (superseded by GSE136555)

description:
****************************
GSM733668 record metadata submitted on May 27 2011 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE136555
****************************

source_name: HMEC

value: primary cell

value: mammary epithelial cell

tag: lab

value: Broad

tag: lab description

value: Bernstein - Broad Institute

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell organism

value: human

tag: cell description

value: mammary epithelial cells

tag: cell karyotype

value: normal

tag: cell lineage

value: ectoderm

tag: cell sex

value: U

tag: antibody

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

value: Illumina_GA2e and Illumina_GA2x


title: ChIP-Seq analysis of H3K27me3 in HUES48 cells; Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5683
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669942_BI.HUES48.H3K27me3.Lib_MC_20101025_10--ChIP_MC_20101020_10_ES_cell_HUES_48_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES48 Cell Line, Library Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6584
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2722
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.299
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.355
POISSON_PERCENTILE: 55

**********************************************************************

ANALYSIS FILE NAME: GSM669942_BI.HUES48.H3K27me3.Lib_MC_20101025_10--ChIP_MC_20101020_10_ES_cell_HUES_48_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6794
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES48 H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K27me3 Library Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.2722
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.299
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.355
POISSON_PERCENTILE: 55

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:10--ChIP:MC:20101020:10:ES cell HUES_48:H3K27Me3

value: HUES48 stem cells

tag: sample alias

tag: sample common name

value: HUES48 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: molecule

value: genomic DNA

tag: disease

tag: passage

tag: line

tag: batch

value: ES cell HUES_48-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in HUES 6 cells; Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5642
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669889_BI.HUES6.H3K4me3.Lib_XZ_20101004_02--ChIP_XZ_20100930_02_ES_cell_HUES_6_H3K4Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6548
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6124
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.611
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9982
IROC_PERCENTILE: 40
POISSON_SCORE: 0.631
POISSON_PERCENTILE: 84

**********************************************************************

ANALYSIS FILE NAME: GSM669889_BI.HUES6.H3K4me3.Lib_XZ_20101004_02--ChIP_XZ_20100930_02_ES_cell_HUES_6_H3K4Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6758
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 H3K4me3 e3.1
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K4me3 Library Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6124
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.611
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9982
IROC_PERCENTILE: 40
POISSON_SCORE: 0.631
POISSON_PERCENTILE: 84

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:02--ChIP:XZ:20100930:02:ES cell HUES_6:H3K4Me3

value: HUES6 Cell Line

value: HUES 6

value: ES cell HUES_6-1

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27me3 in HUES 6 cells; Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5616
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5642
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669887_BI.HUES6.H3K27me3.Lib_XZ_20101004_04--ChIP_XZ_20100930_04_ES_cell_HUES_6_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6490
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3046
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3435
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9646
IROC_PERCENTILE: 85
POISSON_SCORE: 0.451
POISSON_PERCENTILE: 75

**********************************************************************

ANALYSIS FILE NAME: GSM669887_BI.HUES6.H3K27me3.Lib_XZ_20101004_04--ChIP_XZ_20100930_04_ES_cell_HUES_6_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6700
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 H3K27me3 e3.1
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K27me3 Library Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3046
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.3435
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9646
IROC_PERCENTILE: 85
POISSON_SCORE: 0.451
POISSON_PERCENTILE: 75

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:04--ChIP:XZ:20100930:04:ES cell HUES_6:H3K27Me3

value: embrionic stem cell

value: KSR

value: genomic DNA


title: NME-Pre TGF-1

tag: cell line background

value: NMumG

tag: cell type

value: normal murine mammary gland cells

tag: transformed by

value: overexpression of EGFR (NME)

tag: stimulated with

value: none (unstimuated control)


title: Lung_asthmatic_pre-placebo (SRC117263)

status: Public on Jan 18 2011

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117263

hyb_protocol: 18 hours at 60°C with constant rotation on Agilent WHG

scan_protocol: Agilent scanner according to the manufacturer’s protocol

data_processing: the data were extracted and normalized according to the default settings of Agilent Feature Extraction 7.5. LOWESS normalization, background subtraction, and ratio computation.

source_name: human lung biopsy_asthmatic_pre-placebo

label_protocol: T7 RNA polymerase single round of linear amplification

extract_protocol: micro total RNA isolation from animal tissues protocol (Qiagen, Valencia, CA)

tag: age

value: M

tag: disease state

value: Asthma

tag: patientid

tag: th2 signature

value: Low

tag: time

value: pre-treatment

tag: treatment protocol

value: Placebo

source_name: Stratagene Universal Human Reference

tag: reference

value: Stratagene Universal Human Reference


title: Lung_asthmatic_post-flovent (SRC117278)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117278

value: High

value: post-treatment

value: Flovent


title: Lung_asthmatic_post-flovent (SRC117257)

description:
Lung biopsy from flovent treated asthmatic, post-treatment
SRC117257


title: Lung_asthmatic_pre-placebo (SRC117204)

description:
Lung biopsy from placebo treated asthmatic, pre-treatment
SRC117204


title: ChIP-Seq analysis of H3K4me3 in HUES 6 cells; Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5622
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM669893_BI.HUES6.H3K4me3.Lib_XZ_20101004_09--ChIP_XZ_20100930_09_ES_cell_HUES_6_H3K4Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6552
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.59
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5944
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9987
IROC_PERCENTILE: 56
POISSON_SCORE: 0.6174
POISSON_PERCENTILE: 76

**********************************************************************

ANALYSIS FILE NAME: GSM669893_BI.HUES6.H3K4me3.Lib_XZ_20101004_09--ChIP_XZ_20100930_09_ES_cell_HUES_6_H3K4Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6762
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: HUES6 H3K4me3 e3.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K4me3 Library Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.59
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.5944
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9987
IROC_PERCENTILE: 56
POISSON_SCORE: 0.6174
POISSON_PERCENTILE: 76

**********************************************************************

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:09--ChIP:XZ:20100930:09:ES cell HUES_6:H3K4Me3

tag: sample alias

tag: sample common name

value: HUES6 Cell Line

tag: lineage

tag: medium

tag: molecule

value: HUES 6

value: ES cell HUES_6-2

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: Lung_asthmatic_pre-flovent (SRC117138)

description:
Lung biopsy from flovent treated asthmatic, pre-treatment
SRC117138

source_name: human lung biopsy_asthmatic_pre-flovent

tag: Sex

value: F

tag: batch

value: Asthma

value: Low

value: pre-treatment

value: Stratagene Universal Human Reference